You do let yourself in for some things, Simon!
I'd forget clear tube, go for plastic pipe (try your local DIY store) for the wtc, that's what's in my Dragonfish. For end caps...either drop Paul Holman (turbulent) an email, he'll turn you up a pair on the lathe from clear lexan, or ask Mark at MMB (Marks Model Bits) for a pair of cast resin ones. Choice is yours, but I prefer Paul's lathe turned ones. He'll also include the O rings as well if you ask him nicely.
Radio boxes can be a nightmare to keep watertight (been there, done that) so go for a cylinder.
For rudder/plane servos, go for HobbyKing 5g ones, about a fiver each, they also do tiny receivers for around a tenner, postage is pretty cheap and delivery times are excellent. For a boat that size, I'd use a brushed 280 motor, maybe a 360, and for an esc, an ACTion Electronics Pico (www.action-electronics.co.uk) a microscopic little thing for about fifteen quid.
Batteries...an endless choice. Lipos...AAA sized NiMhs...mobile phone batteries...use what you feel happy with and what will fit.